IsotopicDistributionN: Isotopic Distribution of a Nitrogen-15 Labeled Peptide.
In OrgMassSpecR: Organic Mass Spectrometry

Description Usage Arguments Details Value Author(s) References See Also Examples

Simulates the isotopic distribution of a nitrogen-15 labeled peptide. Intended for peptides from proteins grown in media with, for example, nitrogen-15 labeled ammonium chloride as the only nitrogen source.

1 2	IsotopicDistributionN(sequence, incorp, IAA = TRUE, charge = 1, custom = list(code = NULL, elements = NULL))

`sequence`	character vector specifying the amino acid sequence.
`incorp`	numeric value from 0 to 1, specifying the fraction of nitrogen-15.
`IAA`	logical. `TRUE` specifies iodoacetylated cysteine and `FALSE` specifies unmodified cystine.
`charge`	numeric value specifying the number of positive charges. Must be 1, 2, or 3. One proton per charge is added to the amino acid sequence ([M + nH]n+).
`custom`	a list specifying a user defined residue as `custom = list(code, elements)`, where `code` is a one letter character vector representing the custom residue and `elements` is a vector of the number of elements in the character vector, with the indicies equal to C,H,N,O,S,or P.

The amino acid residues must be specified by the one letter codes defined in the help for Digest. If a custom residue code is identical to a predefined residue code, the custom residue will NOT be used in place of the predefined residue; doing so will cause errors.

The natural nitrogen-15 incorporation is 0.00368.

The argument IAA specifies treatment of the protein with iodoacetamide. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S). The nitrogen(s) added is not labeled.

The algorithm used in this function is based on sample, and will give a slightly different result each time it is run. It is similar to the algorithm used in reference 1. IsotopicDistributionN has not been tested for sequences over approximately 3000 amu and charges greater that 3+.

A data frame with the following column names.

`mz`	the m/z value
`intensity`	the number of counts at each m/z value. The total is 10000.
`percent`	the intensity at each m/z value, expressed as a percent of the maximum intensity.

Nathan G. Dodder

1. "Method for Estimating the Isotopic Distributions of Metabolically Labeled Proteins by MALDI-TOFMS: Application to NMR Samples." Choudhary K, Spicer VL, Donald LJ, Duckworth HW, Ens W, Loewen PC, Standing KG, Analytical Chemistry, 2006, 78, 5419-5423.

2. "Perturbation and Interpretation of Nitrogen Isotope Distribution Patterns in Proteomics" Snijders APL, de Koning B, Wright PC, Journal of Proteome Research, 2005, 4, 2185-2191.

3. "Measurement of the Isotope Enrichment of Stable Isotope-Labeled Proteins Using High-Resolution Mass Spectra of Peptides" MacCoss MJ, Wu CC, Matthews DE, and Yates III JR, Analytical Chemistry, 2005, 77, 7646-7653.

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.

Note that in reference 3 "a biologically relevant 13C/12C isotope ratio of 1.096% was used instead of the more carbonate specific ratio of 1.112%." The 13C/12C ratio used by IsotopicDistributionN is 1.081%.

IsotopicDistribution, IsotopicDistributionHDX, sample

## simulate a peptide with 0.368 to 100 percent incorporation and plot
dn <- IsotopicDistributionN("NECFLQHK", incorp = 0.00368)
dn$t <- "incorp = 0.368%"
d50 <- IsotopicDistributionN("NECFLQHK", incorp = 0.5)
d50$t <- "incorp = 50%"
d99 <- IsotopicDistributionN("NECFLQHK", incorp = 0.99)
d99$t <- "incorp = 99%"
x <- rbind(dn, d50, d99)
library(lattice)
xyplot(percent ~ mz | t, data = x,
    type = "h", 
    xlab = "m/z", 
    ylab = "intensity (%)",
    main = "Isotopic distribution of peptide NECFLQHK with 
            varying nitrogen-15 incorporation")
## Not run:          
## simulate peptide DVFLGMFLYPYAR with oxidized methionine
IsotopicDistributionN("DVFLGmFLYPYAR", incorp = 0.5, 
                      custom = list(code = "m", 
                                    elements = c(C=5, H=9, N=1, O=2, S=1)))

## End(Not run)